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For isoform analysis, the Database for Annotation, Visualization and Integrated Discovery (DAVID) (DAVID bioinformatics resources 6.7) was used [ 39].
Pathway Analysis The Database for Annotation, Visualization and Integrated Discovery (DAVID) was used to determine protein family and KEGG pathway enrichment (Huang et al., 2009 ).
The differentially expressed genes were subjected to Ingenuity Pathway analysis, the Database for Annotation, Visualization and Integrated Discovery (DAVID) analysis, the Promoter Analysis and Interaction Network Toolset (PAINT) and Oncomine analysis.
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We performed four separate types of pathway analysis using gene set enrichment analysis (GSEA), the Database for Annotation, Visualization and Integrated Discovery (DAVID), Literature Lab Analysis (LLA), and Ingenuity Pathway Analysis (IPA).
In order to uncover changes in groups of functionally interconnected genes we utilised two online analysis tools the Database for Innovation, Visualization and Integrated Discovery (DAVID; [61] and Ingenuity Pathway Analysis (IPA).
The online analysis tools The Database for Annotation, Visualization and Integrated Discovery (DAVID; [61] and Ingenuity Pathway Analysis (IPA; from Ingenuity Systems Inc., Redwood City, USA; http://www.ingenuity.com) were used to uncover changes in functionally interconnected genes from a list of the most differentially expressed genes (Further description in Text S1).
The lists of targets were imported into Ingenuity pathway analysis (IPA) version 8.0 (IPA, QIAGEN, Redwood City, www.qiagen.com/ingenuity) for canonical pathway analysis or the Database for Annotation, Visualization and Integrated Discovery (DAVID) 6.2.
Biological pathway analysis using the Database for Annotation, Visualization and Integrated Discovery (DAVID) v6.7.
Descriptive analysis of the database for the period January 2003 June 2004.
The targets were analyzed by functional analysis using the Database for Annotation, Visualization and Integrated Discovery (DAVID) version 6.7 [ 33, 34].
A second approach to annotation enrichment analysis used the Database for Annotation, Visualization and Integrated Discovery (DAVID) tool.
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